www.mf.um.si | mf@um.si | t +386 2 2345 821 | f +386 2 2345 820 | - PDF document

Taborska ulica 8 SI - 2000 Maribor, Slovenia www.mf.um.si | mf@um.si | t +386 2 2345 821 | f +386 2 2345 820 | IBAN:SI56 0110 0600 0008 753 | VAT no. SI71674705 | SWIFT: BSLJSI2X

CENTER FOR HUMAN MOLECULAR GENETICS AND PHARMACOGENOMICS & DEPARTMENT FOR BIOCHEMISTRY AND NUTRITION HEAD OF DEPARTMENT Full Prof. Uroš Potočnik, PhD TEAM Asist. Prof. Katja Repnik, PhD Asist. Prof. Helena Čelešnik, PhD Asist. Mario Gorenjak, PhD Asist. Matjaž Deželak, PhD Asist. Prof. Vojko Berce, PhD Asist. Staša Jurgec, BSc Carina Pinto Kozmus, MSc., PhD student Larisa Zemljič, BSc., PhD student Gregor Jezernik, MSc., PhD student Team and head of department LIST AND DESCRIPTION OF LABORATORY EQUIPMENT 1. Next generation sequencing system for DNA sequence analysis (Illumina MiSeq) enables genome- wide analysis with a capacity of 15Gbp in one run. The system is capable of simultaneous in a single experiment diagnosis of most rare hereditary diseases and detection of novel rare DNA polymorphisms that act as genetic risk factors for chronic disease pathogenesis. It also enables the quantification of gene expression and detection of new RNA transcriptions.

2. Real-time PCR system and digital PCR (Life Technologies QuantStudio 12K Flex) is used for effective genotyping of DNA single nucleotide polymorphisms (SNP) using the Taqman method (up to 110,000 genotypes per day) and detection of somatic mutations in cancer. The system is used for gene expression analysis and ncRNA profiling such as miRNA. REASEARCH INTERESTS AND POTENTIAL FOR COLLABORATION • Genetic risk factors (susceptibility to complex diseases) • Molecular mechanisms of disease pathogenesis • Molecular targets for development of new generation of biological drugs • Molecular diagnostics including diseases subtypes • Prognostic factors for disease development • Correlations between treatment response and genetic predisposition (pharmacogenetics and pharmacogenomics) for personalized medicine to maximize treatment efficiency and avoid adverse drug reactions • Identification of genetic susceptibility to complex disease and treatment response (ex. inflammatory bowel diseases, asthma and aspirin intolerance, colon adenoma, rheumatoid arthritis, celiac disease, multiple sclerosis, osteoarthritis, uterine leiomyoma, breast cancer, chronic kidney disease etc.) • Development of biobanks with integrated bioinformatic tools for discovery of genotype/phenotype correlations • Development of high throughput, reliable and cost effective genotyping including high resolution melting curve analysis • Development of applications for quantitative gene expression using Real time PCR and for determination of global gene expression profiles using microarrays (biochips) • Identification of genetic susceptibility to complex diseases and disease clinical features using Single nucleotide polymorphisms (SNP) and haplotype analysis • Discovery of most efficient genetic and gene expression profiles as disease prognostic and diagnostic biomarkers • Collaboration with clinical institutions for knowledge transfer into clinical practice for the benefit of the patients • Genetic analysis and functional cell models ACHIEVEMENTS Prof. Uroš Potočnik and Mitja Mitrovič were coauthors of an article published in Nature, which reported 163 gene loci associated with inflammatory bowel diseases (IBD). The study took part in an international consortium of IBD genetics and has identified the so far largest number of associated gene loci for any disease. This is unsurprising considering that the study is one of the largest genome- wide association studies conducted so far with enrolled more than 75000 patients and controls. The Nature paper received more than 1000 citations in just 3 years and is currently most cited paper at University of Maribor.

RESEARCH PROJECTS INTERNATIONAL COLLABORATION 1. SySPharmPhedia »“Systems p harmacology approach to difficult-to- treat pediatric asthma” call ERA-Net ERACoSysMed "Collaboration on systems medicine funding to promote the implementation of systems biology approaches in clinical research and medical practice, (U. Potočnik coordinator for Slovenian partner, Neatherland, Spain, Germany); 2016 -2019; 2. SFRH/BD/79804/2011: The endocannabinoid system in asthma patients and the effect of cannabinoids in the modulation of inflammatory response: supported by Ministry of Science, Portugal, (he ad of project and mentor: U. Potočnik, PhD student Carina Pinto Kozmus, 2012 -2016); 3. BI-US/15-16-061 SLO- USA, (head dr. Uroš Potočnik) “Genetics and pharmacogenomics of chronic immune diseases”, collaboration with New York Genome Center, USA (Dr. Tuuli L appalainen), 2015-2016; 4. International Inflammatory bowel disease Genetics consortium (IIBDGC) (Slovene national consortium coordinator prof. Uroš Potočnik) . NATIONAL PROJECTS • J3- 6785 “Genetics and pharmacogenomics of Inflammatory bowel diseases and genetically related chronic immune diseases” (head dr. Uroš Potočnik), 2014 -2017; • J3- 6789 “Pathogenic mechanism of the C9orf72 expanded hexanucleotide repeat mutation in neurodegeneration; 2014-2017; • IRP-2013: Genetics of self-injury behavior; (Collaboration with University Clinical Center Maribor head UKC MB T. Bunderla; head of project at MF MB U. Potočnik); 2013 -2016; • IRP-2014/01-21: Nucleotide polymorphisms in genes SDF- 1ɑ, MMP7, MMP9, TIMP2, RAD18 in MACC1 as prognostic factors for colorectal cancer (head of project at UKC MB M. Horvat; head of project at MF MB U. Potocnik); 2013-2016; • IRP-2014/01-30: Identificaition of monogenic mutations and DNA polymorphisms associated with risk for Parkinson disease in Slovenian patients (Collaboration with University Clinical Center Maribor head of project at UKC MB D. Flisar, head of project at MF MB U. Potocnik); 2014-2017; • IRP-2014/01-29: Identification of mutations and DNA polymorphisms in gene SCN9 in patients with complex regional pain syndrome (Collaboration with University Clinical Center Maribor head UKC MB D. Flisar; head of project at MF MB U. Potočnik); 2014 -2017; • IRP-2015: Genetics of chronic kidney disease; (Collaboration with University Clinical Center Maribor head UKC MB S. Bevc; head of project at MF MB U. Potočnik); 2015 -2017; • IRP-2015: Molecular genetic biomarkers for recurrence of Head and neck cancer; (Collaboration with University Clinical Center Maribor head UKC MB A. Čižmarević; head of project at MF MB U. Potočnik); 2015 -2018; • V3- 1505 “Analysis and development of rare diseases field in Slovenia”, 2015 -2017; • P3- 0067 “Pharmacology and pharmacogenomics” (head of project at MF UL Mojca Kržan; prof. U. Potočnik is authorized coordinator of Pharmacogenomics at MF MB, 2014 -2017); • J3- 2175 “Genetic risk factors and pharmacogenomics of inflammatory bowel diseases” financed by ARRS (head prof. U. Potočnik, 2009 -2012);